ensembl developers meeting september 2008 xosé mª fernández european bioinformatics institute
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Ensembl Developers MeetingEnsembl Developers Meeting
September 2008September 2008
XosXosé Mª Fernándezé Mª FernándezEuropean Bioinformatics InstituteEuropean Bioinformatics Institute
In case of fire
• A continuous alarm will sound
• On hearing the fire alarm evacuate the building
immediately using the nearest fire exit
• Report to fire assembly point under the EBI oak tree
Evacuation procedure
Fire Assembly point(under EBI oak tree)
Fire Assembly point(under EBI oak tree)
You are hereYou are here
ToiletsToilets
4 of 30
• Today• Introduction• Ensembl release cycle• Update: Genebuild, Compara, Functional genomics, Web• Ensembl Genomes
• Tomorrow • Gene build• Core: mapping xref• Compara: Multiple genomic alignments with Pecan• Functional genomics: Annotation pipeline
• Tuesday• Ensembl Genomes • Ensembl Outlook
Meeting OutlineMeeting Outline
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• Gene build Bronwen Aken & Jan-Hinnerk Vogel
• Ensembl Core Ian Longden• Ensembl Compara Javier Herrero• Ensembl funcgen Nathan Johnson
Hands onHands on
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Ensembl - ProjectEnsembl - Project
• Joint project– EMBL – European Bioinformatics Institute (EBI) – Wellcome Trust Sanger Institute
• Produce accurate, automatic genome annotation• Focused on selected eukaryotic genomes • Integrate external (distributed) biological data• Presentation of the analysis to all via the Web at
http://www.ensembl.org • Open distribution of the analysis the community• Development of open, collaborative software (databases
and APIs)
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Ensembl - ProjectEnsembl - Project
• Joint project– EMBL – European Bioinformatics Institute (EBI) – Wellcome Trust Sanger Institute
• Produce accurate, automatic genome annotation• Focused on selected eukaryotic genomes • Integrate external (distributed) biological data• Presentation of the analysis to all via the Web at
http://www.ensembl.org • Open distribution of the analysis the community• Development of open, collaborative software (databases and
APIs)
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Ensembl - ProjectEnsembl - Project
• Joint project– EMBL – European Bioinformatics Institute (EBI) – Wellcome Trust Sanger Institute
• Produce accurate, automatic genome annotation• Focused on selected eukaryotic genomes • Integrate external (distributed) biological data• Presentation of the analysis to all via the Web at
http://www.ensembl.org • Open distribution of the analysis the community• Development of open, collaborative software (databases and
APIs)
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EnsemblEnsembl v50v50
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The family is growing!The family is growing!
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Ensembl - ProjectEnsembl - Project
• Joint project– EMBL – European Bioinformatics Institute (EBI) – Wellcome Trust Sanger Institute
• Produce accurate, automatic genome annotation• Focused on selected eukaryotic genomes • Integrate external (distributed) biological data• Presentation of the analysis to all via the Web at
http://www.ensembl.org • Open distribution of the analysis the community• Development of open, collaborative software (databases and
APIs)
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IntegrationIntegration
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Release processRelease process
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Ensembl - ProjectEnsembl - Project
• Joint project– EMBL – European Bioinformatics Institute (EBI) – Wellcome Trust Sanger Institute
• Produce accurate, automatic genome annotation• Focused on selected eukaryotic genomes • Integrate external (distributed) biological data• Presentation of the analysis to all via the Web at
http://www.ensembl.orghttp://www.ensembl.org • Open distribution of the analysis the community• Development of open, collaborative software (databases and
APIs)
15 of 30
Ensembl - ProjectEnsembl - Project
• Joint project– EMBL – European Bioinformatics Institute (EBI) – Wellcome Trust Sanger Institute
• Produce accurate, automatic genome annotation• Focused on selected eukaryotic genomes • Integrate external (distributed) biological data• Presentation of the analysis to all via the Web at
http://www.ensembl.org • Open distribution of the analysis the community• Development of open, collaborative software (databases and
APIs)
16 of 30
Ensembl - ProjectEnsembl - Project
• Joint project– EMBL – European Bioinformatics Institute (EBI) – Wellcome Trust Sanger Institute
• Produce accurate, automatic genome annotation• Focused on selected eukaryotic genomes • Integrate external (distributed) biological data• Presentation of the analysis to all via the Web at
http://www.ensembl.org • Open distribution of the analysis the community• Development of open, collaborative software (databases
and APIs)
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Ensembl’s roadmapEnsembl’s roadmap
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It ain’t a simple thingIt ain’t a simple thing
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Putting the blocks togetherPutting the blocks together
Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team
Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team
Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team
Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team
Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team
Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team
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Ensembl – release cycleEnsembl – release cycle
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• Hardware upgrade– Performance improvement
• New look & feel– Design changes
– Control panel across all pages
• Hidden goodies: Store your own data
http://beta.ensembl.orghttp://beta.ensembl.org
Ensembl from insideEnsembl from inside
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Bronwen & JanBronwen & Jan• Running the Ensembl
gene build pipeline
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JavierJavier• Multiple Alignments with Pecan • Constrained elements• Conservation scores
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NathanNathan• Functional Genomics
Annotation pipeline
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IanIan• Mapping xrefs
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AnneAnne• Web update
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PerlApplications Compara
Pipeline
ensj Java*
martj Java
martp Perl
EnsemblPipeline
EnsemblWeb Site
Apollo
JavaApplications
Variation
Compara
BioMart
User API Layer Database
Core
Core
BioDas Perl
ProServerDazzleLDAS
Variation
FunctgenFunctGen
API NetworkAPI Network
BioConductor
biomaRt
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Wrap upWrap up
• Paul will outline some developments in the pipeline for the new year (Tuesday)
• And some of you will share your Ensembl experience with us…
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Ensembl TeamEnsembl TeamJuly 2006July 2006
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Ensembl TeamEnsembl Team
September 2008September 2008
Ensembl Paul Flicek (EBI), Steve Searle (Sanger Institute)
Vertebrate Genomics Mario Caccamo, Laura Clark, Jonathan Hinton, Zam Iqbal, Vasudev Kumanduri, Ilkka Lappalainen
SoftwareGlenn Proctor, Syed Haider, Andrew Jenkinson, Andreas Kähäri, Stephen Keenan, Rhoda Kinsella, Eugene Kulesha, Ian Longden, Daniel Rios
Comparative Genomics Javier Herrero, Kathryn Beal, Benoît Ballester, Stephen Fitzgerald, Leo Gordon, Albert Vilella
Functional Genomics Nathan Johnson, Stefan Gräf, Steven Wilder
Variation Fiona Cunningham, Yuan Chen
Analysis and Annotation Bronwen Aken, Julio Banet, Susan Fairley, Jan-Hinnerck Vogel, Simon White, Amonida Zadissa
Web Team James Smith, Eugene Bragin, Anne Parker, Bethan Pritchard, Steve Trevanion (VEGA)
Zebrafish Kerstin Howe, Britt Reimholz, James Torrance
VectorBase Dan Lawson, Martin Hammond, Karyn Megy
Outreach Xosé M Fernández, Bert Overduin, Michael Schuster (QC), Giulietta Spudich
Systems & Support Guy Coates, Tim Cutts, Shelley Goddard
Research Ian Dunham, Damian Keefe, Alison Meynert, Dace Ruklisa, Guy Slater, Daniel Zerbino
Ensembl Strategy Ewan Birney, Richard Durbin, Tim Hubbard
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